I'm not saying it's perfect... but to say that shotgun running is ineffective because the option read doesn't work perfectly is extreme. HB Dives & QB Blasts out of flex/offset formations are deadly, especially if you have a nice audible system worked out to take advantage of how the defense lines up. And I've found that versus those teams with the stud DL that wreaks havoc, a good dose of HB Dive & HB Off-Tackle opens up the option game.
I also have never downloaded the patch. Could this have something to do with it?